Nice! Great list of considerations!
Engineers could terraform in Civ4 (I think it was Civ4), turning hills into plains, plains into grassland, and even plains/grassland into hills. That was when I originally got the idea - why can't they reclaim land from the sea?
My thoughts on your excellent questions would be:
1) Can only reclaim coast and adjoining ocean would remain ocean - so you can't just end up reclaiming an entire ocean! (Though your Great Engineer idea also prevents this)
2) I didn't think of that but I do like the idea. Harbours have been blocked and turned into fresh water dams in RL, so that would make sense.
3) I think this would apply only to the extent that one of the AI agendas is currently - Environmentalist and Naturalist.
4) No idea.
5) I would imagine the Appeal of the new tile would be Average or Uninviting. I don't think it should be Disgusting because the aim of reclaiming the land may be to build neighbourhoods (thinking RL Singapore and Hong Kong here), so Disgusting appeal might be counter productive.
6) Arghhh! You have thought about this too hard! Probably easiest if it stays the same continent it is attached to. We might have to ask the UN (but China won't listen to their decision)
7) Complicated. Perhaps it can't be done within 1 tile of a natural wonder?
8) Cliffs gone.
9) Rivers still flow along side of hex as normal. If coastal hexes either side of river "mouth" turned to land the river continues through middle to ocean.
10) Not sure it would have any practical effect on trade routes?
11) If you followed the model from Civ4, the engineers could continue to work on the newly formed plains and turn them into grassland or even hills (or tundra I guess... why would you want tundra?! lol)
Thanks for your excellent suggestions/questions! I have asked some "lower" level modders and they said it was beyond them, so maybe this can only be done at Firaxis/Y2K level? (I have no idea!)